| 1. |
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| 2. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Craddock, Nick, et al.
(författare)
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Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7289, s. 713-720
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Tidskriftsartikel (refereegranskat)abstract
- Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed,19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated similar to 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.
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| 4. |
- Abazajian, Kevork, et al.
(författare)
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CMB-S4 : Forecasting Constraints on Primordial Gravitational Waves
- 2022
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 926:1
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Tidskriftsartikel (refereegranskat)abstract
- CMB-S4—the next-generation ground-based cosmic microwave background (CMB) experiment—is set to significantly advance the sensitivity of CMB measurements and enhance our understanding of the origin and evolution of the universe. Among the science cases pursued with CMB-S4, the quest for detecting primordial gravitational waves is a central driver of the experimental design. This work details the development of a forecasting framework that includes a power-spectrum-based semianalytic projection tool, targeted explicitly toward optimizing constraints on the tensor-to-scalar ratio, r, in the presence of Galactic foregrounds and gravitational lensing of the CMB. This framework is unique in its direct use of information from the achieved performance of current Stage 2–3 CMB experiments to robustly forecast the science reach of upcoming CMB-polarization endeavors. The methodology allows for rapid iteration over experimental configurations and offers a flexible way to optimize the design of future experiments, given a desired scientific goal. To form a closed-loop process, we couple this semianalytic tool with map-based validation studies, which allow for the injection of additional complexity and verification of our forecasts with several independent analysis methods. We document multiple rounds of forecasts for CMB-S4 using this process and the resulting establishment of the current reference design of the primordial gravitational-wave component of the Stage-4 experiment, optimized to achieve our science goals of detecting primordial gravitational waves for r > 0.003 at greater than 5σ, or in the absence of a detection, of reaching an upper limit of r < 0.001 at 95% CL.
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| 5. |
- Ade, Peter, et al.
(författare)
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The Simons Observatory : science goals and forecasts
- 2019
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Ingår i: Journal of Cosmology and Astroparticle Physics. - : IOP Publishing. - 1475-7516. ; :2
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Tidskriftsartikel (refereegranskat)abstract
- The Simons Observatory (SO) is a new cosmic microwave background experiment being built on Cerro Toco in Chile, due to begin observations in the early 2020s. We describe the scientific goals of the experiment, motivate the design, and forecast its performance. SO will measure the temperature and polarization anisotropy of the cosmic microwave background in six frequency bands centered at: 27, 39, 93, 145, 225 and 280 GHz. The initial con figuration of SO will have three small-aperture 0.5-m telescopes and one large-aperture 6-m telescope, with a total of 60,000 cryogenic bolometers. Our key science goals are to characterize the primordial perturbations, measure the number of relativistic species and the mass of neutrinos, test for deviations from a cosmological constant, improve our understanding of galaxy evolution, and constrain the duration of reionization. The small aperture telescopes will target the largest angular scales observable from Chile, mapping approximate to 10% of the sky to a white noise level of 2 mu K-arcmin in combined 93 and 145 GHz bands, to measure the primordial tensor-to-scalar ratio, r, at a target level of sigma(r) = 0.003. The large aperture telescope will map approximate to 40% of the sky at arcminute angular resolution to an expected white noise level of 6 mu K-arcmin in combined 93 and 145 GHz bands, overlapping with the majority of the Large Synoptic Survey Telescope sky region and partially with the Dark Energy Spectroscopic Instrument. With up to an order of magnitude lower polarization noise than maps from the Planck satellite, the high-resolution sky maps will constrain cosmological parameters derived from the damping tail, gravitational lensing of the microwave background, the primordial bispectrum, and the thermal and kinematic Sunyaev-Zel'dovich effects, and will aid in delensing the large-angle polarization signal to measure the tensor-to-scalar ratio. The survey will also provide a legacy catalog of 16,000 galaxy clusters and more than 20,000 extragalactic sources.
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| 6. |
- Aimo, Alberto, et al.
(författare)
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Cardiac remodelling - Part 2: Clinical, imaging and laboratory findings. A review from the Study Group on Biomarkers of the Heart Failure Association of the European Society of Cardiology
- 2022
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Ingår i: European Journal of Heart Failure. - : WILEY. - 1388-9842 .- 1879-0844. ; 24:6, s. 944-958
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Forskningsöversikt (refereegranskat)abstract
- In patients with heart failure, the beneficial effects of drug and device therapies counteract to some extent ongoing cardiac damage. According to the net balance between these two factors, cardiac geometry and function may improve (reverse remodelling, RR) and even completely normalize (remission), or vice versa progressively deteriorate (adverse remodelling, AR). RR or remission predict a better prognosis, while AR has been associated with worsening clinical status and outcomes. The remodelling process ultimately involves all cardiac chambers, but has been traditionally evaluated in terms of left ventricular volumes and ejection fraction. This is the second part of a review paper by the Study Group on Biomarkers of the Heart Failure Association of the European Society of Cardiology dedicated to ventricular remodelling. This document examines the proposed criteria to diagnose RR and AR, their prevalence and prognostic value, and the variables predicting remodelling in patients managed according to current guidelines. Much attention will be devoted to RR in patients with heart failure with reduced ejection fraction because most studies on cardiac remodelling focused on this setting.
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| 7. |
- Gonzalez, Arantxa, et al.
(författare)
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Cardiac remodelling - Part 1: From cells and tissues to circulating biomarkers. A review from the Study Group on Biomarkers of the Heart Failure Association of the European Society of Cardiology
- 2022
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Ingår i: European Journal of Heart Failure. - : WILEY. - 1388-9842 .- 1879-0844. ; 24:6, s. 927-943
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Forskningsöversikt (refereegranskat)abstract
- Cardiac remodelling refers to changes in left ventricular structure and function over time, with a progressive deterioration that may lead to heart failure (HF) development (adverse remodelling) or vice versa a recovery (reverse remodelling) in response to HF treatment. Adverse remodelling predicts a worse outcome, whilst reverse remodelling predicts a better prognosis. The geometry, systolic and diastolic function and electric activity of the left ventricle are affected, as well as the left atrium and on the long term even right heart chambers. At a cellular and molecular level, remodelling involves all components of cardiac tissue: cardiomyocytes, fibroblasts, endothelial cells and leucocytes. The molecular, cellular and histological signatures of remodelling may differ according to the cause and severity of cardiac damage, and clearly to the global trend toward worsening or recovery. These processes cannot be routinely evaluated through endomyocardial biopsies, but may be reflected by circulating levels of several biomarkers. Different classes of biomarkers (e.g. proteins, non-coding RNAs, metabolites and/or epigenetic modifications) and several biomarkers of each class might inform on some aspects on HF development, progression and long-term outcomes, but most have failed to enter clinical practice. This may be due to the biological complexity of remodelling, so that no single biomarker could provide great insight on remodelling when assessed alone. Another possible reason is a still incomplete understanding of the role of biomarkers in the pathophysiology of cardiac remodelling. Such role will be investigated in the first part of this review paper on biomarkers of cardiac remodelling.
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| 8. |
- Jones, Robert P., et al.
(författare)
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Patterns of Recurrence After Resection of Pancreatic Ductal Adenocarcinoma : A Secondary Analysis of the ESPAC-4 Randomized Adjuvant Chemotherapy Trial
- 2019
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Ingår i: JAMA Surgery. - : AMER MEDICAL ASSOC. - 2168-6254 .- 2168-6262. ; 154:11, s. 1038-1048
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Tidskriftsartikel (refereegranskat)abstract
- Importance: The patterns of disease recurrence after resection of pancreatic ductal adenocarcinoma with adjuvant chemotherapy remain unclear.Objective: To define patterns of recurrence after adjuvant chemotherapy and the association with survival.Design, Setting, and Participants: Prospectively collected data from the phase 3 European Study Group for Pancreatic Cancer 4 adjuvant clinical trial, an international multicenter study. The study included 730 patients who had resection and adjuvant chemotherapy for pancreatic cancer. Data were analyzed between July 2017 and May 2019.Interventions: Randomization to adjuvant gemcitabine or gemcitabine plus capecitabine.Main Outcomes and Measures: Overall survival, recurrence, and sites of recurrence.Results: Of the 730 patients, median age was 65 years (range 37-81 years), 414 were men (57%), and 316 were women (43%). The median follow-up time from randomization was 43.2 months (95% CI, 39.7-45.5 months), with overall survival from time of surgery of 27.9 months (95% CI, 24.8-29.9 months) with gemcitabine and 30.2 months (95% CI, 25.8-33.5 months) with the combination (HR, 0.81; 95% CI, 0.68-0.98; P=.03). The 5-year survival estimates were 17.1% (95% CI, 11.6%-23.5%) and 28.0% (22.0%-34.3%), respectively. Recurrence occurred in 479 patients (65.6%); another 78 patients (10.7%) died without recurrence. Local recurrence occurred at a median of 11.63 months (95% CI, 10.05-12.19 months), significantly different from those with distant recurrence with a median of 9.49 months (95% CI, 8.44-10.71 months) (HR, 1.21; 95% CI, 1.01-1.45; P=.04). Following recurrence, the median survival was 9.36 months (95% CI, 8.08-10.48 months) for local recurrence and 8.94 months (95% CI, 7.82-11.17 months) with distant recurrence (HR, 0.89; 95% CI, 0.73-1.09; P=.27). The median overall survival of patients with distant-only recurrence (23.03 months; 95% CI, 19.55-25.85 months) or local with distant recurrence (23.82 months; 95% CI, 17.48-28.32 months) was not significantly different from those with only local recurrence (24.83 months; 95% CI, 22.96-27.63 months) (P=.85 and P=.35, respectively). Gemcitabine plus capecitabine had a 21% reduction of death following recurrence compared with monotherapy (HR, 0.79; 95% CI, 0.64-0.98; P=.03).Conclusions and Relevance: There were no significant differences between the time to recurrence and subsequent and overall survival between local and distant recurrence. Pancreatic cancer behaves as a systemic disease requiring effective systemic therapy after resection.Trial Registration: ClinicalTrials.gov identifier: NCT00058201, EudraCT 2007-004299-38, and ISRCTN 96397434. This secondary analysis of a randomized clinical trial investigates patterns of recurrence after adjuvant chemotherapy in pancreatic cancer and the association with survival.
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| 9. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
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Ingår i: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
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Forskningsöversikt (refereegranskat)abstract
- Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.
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| 10. |
- Majid, Asifa, et al.
(författare)
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Differential coding of perception in the world's languages
- 2018
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424. ; 115:45, s. 11369-11376
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Tidskriftsartikel (refereegranskat)abstract
- Is there a universal hierarchy of the senses, such that some senses (e.g., vision) are more accessible to consciousness and linguistic description than others (e.g., smell)? The long-standing presumption in Western thought has been that vision and audition are more objective than the other senses, serving as the basis of knowledge and understanding, whereas touch, taste, and smell are crude and of little value. This predicts that humans ought to be better at communicating about sight and hearing than the other senses, and decades of work based on English and related languages certainly suggests this is true. However, how well does this reflect the diversity of languages and communities worldwide? To test whether there is a universal hierarchy of the senses, stimuli from the five basic senses were used to elicit descriptions in 20 diverse languages, including 3 unrelated sign languages. We found that languages differ fundamentally in which sensory domains they linguistically code systematically, and how they do so. The tendency for better coding in some domains can be explained in part by cultural preoccupations. Although languages seem free to elaborate specific sensory domains, some general tendencies emerge: for example, with some exceptions, smell is poorly coded. The surprise is that, despite the gradual phylogenetic accumulation of the senses, and the imbalances in the neural tissue dedicated to them, no single hierarchy of the senses imposes itself upon language.
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| 11. |
- Nguyen, Thanh N, et al.
(författare)
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Global Impact of the COVID-19 Pandemic on Stroke Volumes and Cerebrovascular Events: A 1-Year Follow-up.
- 2023
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Ingår i: Neurology. - 1526-632X. ; 100:4
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Tidskriftsartikel (refereegranskat)abstract
- Declines in stroke admission, IV thrombolysis (IVT), and mechanical thrombectomy volumes were reported during the first wave of the COVID-19 pandemic. There is a paucity of data on the longer-term effect of the pandemic on stroke volumes over the course of a year and through the second wave of the pandemic. We sought to measure the effect of the COVID-19 pandemic on the volumes of stroke admissions, intracranial hemorrhage (ICH), IVT, and mechanical thrombectomy over a 1-year period at the onset of the pandemic (March 1, 2020, to February 28, 2021) compared with the immediately preceding year (March 1, 2019, to February 29, 2020).We conducted a longitudinal retrospective study across 6 continents, 56 countries, and 275 stroke centers. We collected volume data for COVID-19 admissions and 4 stroke metrics: ischemic stroke admissions, ICH admissions, IVT treatments, and mechanical thrombectomy procedures. Diagnoses were identified by their ICD-10 codes or classifications in stroke databases.There were 148,895 stroke admissions in the 1 year immediately before compared with 138,453 admissions during the 1-year pandemic, representing a 7% decline (95% CI [95% CI 7.1-6.9]; p < 0.0001). ICH volumes declined from 29,585 to 28,156 (4.8% [5.1-4.6]; p < 0.0001) and IVT volume from 24,584 to 23,077 (6.1% [6.4-5.8]; p < 0.0001). Larger declines were observed at high-volume compared with low-volume centers (all p < 0.0001). There was no significant change in mechanical thrombectomy volumes (0.7% [0.6-0.9]; p = 0.49). Stroke was diagnosed in 1.3% [1.31-1.38] of 406,792 COVID-19 hospitalizations. SARS-CoV-2 infection was present in 2.9% ([2.82-2.97], 5,656/195,539) of all stroke hospitalizations.There was a global decline and shift to lower-volume centers of stroke admission volumes, ICH volumes, and IVT volumes during the 1st year of the COVID-19 pandemic compared with the prior year. Mechanical thrombectomy volumes were preserved. These results suggest preservation in the stroke care of higher severity of disease through the first pandemic year.This study is registered under NCT04934020.
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| 12. |
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| 13. |
- Abernethy, R. J., et al.
(författare)
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Poly(methimazolyl)borato nitrosyl complexes of molybdenum and tungsten
- 2008
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Ingår i: Organometallics. - : American Chemical Society (ACS). - 0276-7333 .- 1520-6041. ; 27:17, s. 4455-4463
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Tidskriftsartikel (refereegranskat)abstract
- The syntheses of a range of poly(methimazolyl)borate -ligated nitrosyl complexes of tungsten and molybdenum are reported, the characterization of which includes the crystal structure determinations of the compounds [W(NO)(CO)(2){k(3)-S,S',S''-HB(mt)(3)}], [W(NO)(CO)(2)(PPh3){k(2)-S,S'-H2B(mt)(2)}], and [Mo(NO-)(CO)(2) {k(3)-H,S,S'-H2B(mt)(2)}] (mt = methimazoyl). The reaction of [W(NO)(CO)(3)(PPh3)(2)]PF6 with Na[HB(mt)(3)] and Na[H2B(mt)(2)}] provides respectively [W(NO)(CO)(2)[HB(mt)(3)] and [W(NO)(CO)(2)(PPh3){k(2_) S,S'-H2B(mt)(2)}]. The complexes [M(NO)(CO)(2){HB(mt)(3)}] and [M(NO)(CO)(2){k(3)-H,S,S'-H2B(mt)(2)}] (M = W, Mo) arise from the reactions of Na[M(CO)(3){H2B(mt)(2)}] with N-methyl-N-nitrosotoluenesulfonamide. The molybdenum complex [Mo(NO)(CO)(2){HB(mt)(3)}] is also obtained unexpectedly from the reaction of [MO(eta(3)-C3H5)(CO)(2){HB(mt)(3)}] with [NO]BF4.
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| 14. |
- Abernethy, Robyn J., et al.
(författare)
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Relative hemilabilities of H2B(az)2 (az = pyrazolyl, dimethylpyrazolyl, methimazolyl) chelates in the complexes [M(η-C3H5)(CO)2{H2B(az)2}] (M = Mo, W)
- 2020
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Ingår i: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; 49:3, s. 781-796
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Tidskriftsartikel (refereegranskat)abstract
- The reactions of [M(η3-C3H5)Br(CO)2(NCMe)2] (M = Mo, W) or [Mo(η3-C3H5)Br(CO)2(PMe2Ph)2] with Na[H2B(mt)2] (mt = methimazolyl) affords the complexes [M(η3-C3H5)(CO)2{κ3-H,S,S′-H2B(mt)2}], the 3-centre, 2-electron B-H-M interaction of which was found to be inert with respect to opening under mild conditions, while more forcing conditions (heating with PMe2Ph) resulted in cleavage of the entire allyl and borate ligands to form [Mo(CO)3(PMe2Ph)3]. In contrast, the reaction of [Mo(η3-C3H5)Br(CO)2(NCMe)2] with Na[H2B(pz)2] affords either [Mo(η3-C3H5)(CO)2{κ3-H,N,N′-H2B(pz)2}] or (more likely) [Mo(η3-C3H5)(CO)2(NCMe){κ2-N,N′-H2B(pz)2}] which in turn reacts with phosphines to provide [[Mo(η3-C3H5)(CO)2(PPhR2){κ2-N,N′-H2B(pz)2}] (R = Me, Ph). The reactions discussed indicate the propensity for 3-centre, 2-electron B-H-Mo interactions increases in the order H2B(pz)2 < H2B(pz∗)2 < H2B(mt)2 (pz∗ = 3,5-dimethypyrazolyl).
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| 15. |
- Adcox, K, et al.
(författare)
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Centrality dependence of the high (PT) charged hadron suppression in Au+Au collisions at root s(NN)=130 GeV
- 2003
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Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - 0370-2693. ; 561:1-2, s. 82-92
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Tidskriftsartikel (refereegranskat)abstract
- PHENIX has measured the centrality dependence of charged hadron p(T) spectra from Au +An collisions at root(s)NN = 130 GeV The truncated mean p(T) decreases with centrality for p(T) > 2 GeV/c, indicating an apparent reduction of the contribution from hard scattering to high p(T) hadrdn production. For central collisions the yield at high p(T) is shown to be suppressed compared to binary nucleon-nucleon collision scaling of p + p, data. This suppression is monotonically increasing with centrality, but most of the change occurs below 30% centrality, i.e., for collisions with less than similar to140 participating nucleons. The observed p(T) and centrality dependence is consistent with the particle production predicted by models including hard scattering and subsequent energy loss of the scattered partons in the dense matter created in the collisions. (C) 2003 Published by Elsevier Science B.V.
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| 16. |
- Adcox, K, et al.
(författare)
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Event-by-event fluctuations in mean p(T) and mean E(T) in root s(NN)=130 GeVAu+Au collisions
- 2002
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Ingår i: Physical Review C (Nuclear Physics). - 0556-2813. ; 66:2
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Tidskriftsartikel (refereegranskat)abstract
- Distributions of event-by-event fluctuations of the mean transverse momentum and mean transverse energy near mid-rapidity have been measured in Au+Au collisions at roots(NN)=130 GeV at the Relativistic Heavy-Ion Collider. By comparing the distributions to what is expected for statistically independent particle emission, the magnitude of nonstatistical fluctuations in mean transverse momentum is determined to be consistent with zero. Also, no significant nonrandom fluctuations in mean transverse energy are observed. By constructing a fluctuation model with two event classes that preserve the mean and variance of the semi-inclusive p(T) or e(T) spectra, we exclude a region of fluctuations in roots(NN)=130 GeV Au+Au collisions.
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| 17. |
- Adcox, K, et al.
(författare)
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Flow Measurements via Two-Particle Azimuthal Correlations in Au+Au Collisions at sqrt[sNN]=130 GeV
- 2002
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Ingår i: Physical Review Letters. - 1079-7114. ; 89
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Tidskriftsartikel (refereegranskat)abstract
- Two-particle azimuthal correlation functions are presented for charged hadrons produced in Au+Au collisions at the Relativistic Heavy Ion Collider (sqrt[sNN]=130 GeV). The measurements permit determination of elliptic flow without event-by-event estimation of the reaction plane. The extracted elliptic flow values (v2) show significant sensitivity to both the collision centrality and the transverse momenta of emitted hadrons, suggesting rapid thermalization and relatively strong velocity fields. When scaled by the eccentricity of the collision zone ε, the scaled elliptic flow shows little or no dependence on centrality for charged hadrons with relatively low pT. A breakdown of this ε scaling is observed for charged hadrons with pT >1.0 GeV/c.
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| 18. |
- Adcox, K, et al.
(författare)
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Formation of dense partonic matter in relativistic nucleus-nucleus collisions at RHIC: Experimental evaluation by the PHENIX Collaboration
- 2005
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Ingår i: Nuclear Physics, Section A. - : Elsevier BV. - 0375-9474. ; 757:1-2, s. 184-283
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Forskningsöversikt (refereegranskat)abstract
- Extensive experimental data from high-energy nucleus-nucleus collisions were recorded using the PHENIX detector at the Relativistic Heavy Ion Collider (RHIC). The comprehensive set of measurements from the first three years of RHIC operation includes charged particle multiplicities, transverse energy, yield ratios and spectra of identified hadrons in a wide range of transverse momenta (PT), elliptic flow, two-particle correlations, nonstatistical fluctuations, and suppression of particle production at high PT. The results are examined with an emphasis on implications for the formation of a new state of dense matter. We find that the state of matter created at RHIC cannot be described in terms of ordinary color neutral hadrons.
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| 19. |
- Adcox, K, et al.
(författare)
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Measurement of Lambda and (Lambda)over-bar particles in Au plus Au collisions at root s(NN)=130 GeV
- 2002
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Ingår i: Physical Review Letters. - 1079-7114. ; 89:9
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Tidskriftsartikel (refereegranskat)abstract
- We present results on the measurement of Lambda and (&ULambda;) over bar production in Au+Au collisions at roots(NN)=130 GeV with the PHENIX detector at the Relativistic Heavy Ion Collider. The transverse momentum spectra were measured for minimum bias and for the 5% most central events. The (&ULambda;) over bar/Lambda ratios are constant as a function of p(T) and the number of participants. The measured net Lambda density is significantly larger than predicted by models based on hadronic strings (e.g., HIJING) but in approximate agreement with models which include the gluon-junction mechanism.
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| 20. |
- Adcox, K, et al.
(författare)
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Measurement of single electrons and implications for charm production in Au+Au collisions at root(NN)-N-S=130 GeV
- 2002
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Ingår i: Physical Review Letters. - 1079-7114. ; 88:19
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Tidskriftsartikel (refereegranskat)abstract
- Transverse momentum spectra of electrons from Au+Au collisions at roots(NN) = 130 GeV have been measured at midrapidity by the PHENIX experiment at the Relativistic Heavy Ion Collider. The spectra show an excess above the background from photon conversions and light hadron decays. The electron signal is consistent with that expected from semileptonic decays of charm. The yield of the electron signal dN(e)/dy for p(T) > 0.8 GeV/c is 0.025 +/- 0.004(stat) +/- 0.010( syst) in central collisions, and the corresponding charm cross section is 380 +/- 60(stat) +/- 200(syst ) mub per binary nucleon-nucleon collision.
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| 21. |
- Adcox, K, et al.
(författare)
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Net charge fluctuations in Au+Au interactions root s(NN)=130 GeV
- 2002
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Ingår i: Physical Review Letters. - 1079-7114. ; 89
-
Tidskriftsartikel (refereegranskat)abstract
- Data from Au+ Au interactions at s(NN)=130 GeV, obtained with the PHENIX detector at the Relativistic Heavy-Ion Collider, are used to investigate local net charge fluctuations among particles produced near midrapidity. According to recent suggestions, such fluctuations may carry information from the quark-gluon plasma. This analysis shows that the fluctuations are dominated by a stochastic distribution of particles, but are also sensitive to other effects, like global charge conservation and resonance decays.
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| 22. |
- Adcox, K, et al.
(författare)
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PHENIX detector overview
- 2003
-
Ingår i: Nuclear Instruments & Methods in Physics Research. Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment. - 0167-5087. ; 499:2-3, s. 469-479
-
Tidskriftsartikel (refereegranskat)abstract
- The PHENIX detector is designed to perform a broad study of A-A, p-A, and p-p collisions to investigate nuclear matter under extreme conditions. A wide variety of probes, sensitive to all timescales, are used to study systematic variations with species and energy as well as to measure the spin structure of the nucleon. Designing for the needs of the heavy-ion and polarized-proton programs has produced a detector with unparalleled capabilities. PHENIX measures electron and muon pairs, photons, and hadrons with excellent energy and momentum resolution. The detector consists of a large number of subsystems that are discussed in other papers in this volume. The overall design parameters of the detector are presented. (C) 2002 Elsevier Science B.V. All rights reserved.
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| 23. |
- Adcox, K, et al.
(författare)
-
Suppression of hadrons with large transverse momentum in central Au+Au collisions at root s(NN)=130 GeV
- 2002
-
Ingår i: Physical Review Letters. - 1079-7114. ; 88:2
-
Tidskriftsartikel (refereegranskat)abstract
- Transverse momentum spectra for charged hadrons and for neutral pions in the range 1 Gev/c < P-T < 5 GeV/c have been measured by the PHENIX experiment at RHIC in Au + Au collisions at rootS(NN) = 130 GeV. At high p(T) the spectra from peripheral nuclear collisions are consistent with scaling the spectra from p + p collisions by the average number of binary nucleon-nucleon collisions. The spectra from central collisions are significantly suppressed when compared to the binary-scaled p + p expectation, and also when compared to similarly binary-scaled peripheral collisions, indicating a novel nuclear-medium effect in central nuclear collisions at RHIC energies.
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| 24. |
- Adcox, K, et al.
(författare)
-
Transverse-mass dependence of two-pion correlations in Au+Au collisions at root(NN)-N-S=130 GeV
- 2002
-
Ingår i: Physical Review Letters. - 1079-7114. ; 88:19
-
Tidskriftsartikel (refereegranskat)abstract
- Two-pion correlations in roots(NN) = 130 GeV Au+Au collisions at RHIC have been measured over a broad range of pair transverse momentum k(T) by the PHENIX experiment at RHIC. The k(T) dependent transverse radii are similar to results from heavy-ion collisions at roots(NN) = 4.1 , 4.9, and 17.3 GeV, whereas the longitudinal radius increases monotonically with beam energy. The ratio of the outwards to sidewards transverse radii (R-out/R-side) is consistent with unity and independent of k(T) .
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| 25. |
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| 26. |
- Ballantyne, Kaye N., et al.
(författare)
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Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats
- 2014
-
Ingår i: Human Mutation. - : John Wiley & Sons. - 1059-7794 .- 1098-1004. ; 35:8, s. 1021-1032
-
Tidskriftsartikel (refereegranskat)abstract
- Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, greater than99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836-0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father-son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RMY-STRs in identifying and separating unrelated and related males and provides a reference database.
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| 27. |
- Bauerschmidt, Christina, et al.
(författare)
-
Cohesin phosphorylation and mobility of SMC1 at ionizing radiation-induced DNA double-strand breaks in human cells
- 2011
-
Ingår i: Experimental Cell Research. - : Elsevier BV. - 0014-4827 .- 1090-2422. ; 317:3, s. 330-337
-
Tidskriftsartikel (refereegranskat)abstract
- Cohesin, a hetero-tetrameric complex of SMC1, SMC3, Rad21 and Scc3, associates with chromatin after mitosis and holds sister chromatids together following DNA replication. Following DNA damage, cohesin accumulates at and promotes the repair of DNA double-strand breaks. In addition, phosphorylation of the SMC1/3 subunits contributes to DNA damage-induced cell cycle checkpoint regulation. The aim of this study was to determine the regulation and consequences of SMC1/3 phosphorylation as part of the cohesin complex. We show here that the ATM-dependent phosphorylation of SMC1 and SMC3 is mediated by H2AX, 53BP1 and MDC1. Depletion of RAD21 abolishes these phosphorylations, indicating that only the fully assembled complex is phosphorylated. Comparison of wild type SMC1 and SMC1S966A in fluorescence recovery after photo-bleaching experiments shows that phosphorylation of SMC1 is required for an increased mobility after DNA damage in G2-phase cells, suggesting that ATM-dependent phosphorylation facilitates mobilization of the cohesin complex after DNA damage.
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| 28. |
- Baxter, Amanda L., et al.
(författare)
-
Collaborative experience between scientific software projects using Agile Scrum development
- 2022
-
Ingår i: Software, practice & experience. - : John Wiley & Sons. - 0038-0644 .- 1097-024X. ; 52:10, s. 2077-2096
-
Tidskriftsartikel (refereegranskat)abstract
- Developing sustainable software for the scientific community requires expertise in software engineering and domain science. This can be challenging due to the unique needs of scientific software, the insufficient resources for software engineering practices in the scientific community, and the complexity of developing for evolving scientific contexts. While open-source software can partially address these concerns, it can introduce complicating dependencies and delay development. These issues can be reduced if scientists and software developers collaborate. We present a case study wherein scientists from the SuperNova Early Warning System collaborated with software developers from the Scalable Cyberinfrastructure for Multi-Messenger Astrophysics project. The collaboration addressed the difficulties of open-source software development, but presented additional risks to each team. For the scientists, there was a concern of relying on external systems and lacking control in the development process. For the developers, there was a risk in supporting a user-group while maintaining core development. These issues were mitigated by creating a second Agile Scrum framework in parallel with the developers' ongoing Agile Scrum process. This Agile collaboration promoted communication, ensured that the scientists had an active role in development, and allowed the developers to evaluate and implement the scientists' software requirements. The collaboration provided benefits for each group: the scientists actuated their development by using an existing platform, and the developers utilized the scientists' use-case to improve their systems. This case study suggests that scientists and software developers can avoid scientific computing issues by collaborating and that Agile Scrum methods can address emergent concerns.
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| 29. |
- Berg, Erik, 1970-
(författare)
-
Efficient and Flexible Characterization of Data Locality through Native Execution Sampling
- 2005
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Data locality is central to modern computer designs. The widening gap between processor speed and memory latency has introduced the need for a deep hierarchy of caches. Thus, the performance of an application is to a large extent dependent on the amount of data locality the caches can exploit. Some data locality comes naturally from the way most programs are written and the way their data is allocated in the memory. Compilers further try to create data locality by loop transformations and optimized data layout. Different ways of writing a program and/or laying out its data may improve an application’s locality even more. However, it is far from obvious how such a locality optimization can be achieved, especially since the optimizing compiler may have left the optimization job half done. Thus, efficient tools are needed to guide the software developers on their quest for data locality. The main contribution of this dissertation is a sample-based novel method for analyzing the data locality of an application. Very sparse data is collected during a single execution of the studied application. The sparse sampling adds a minimum overhead to the execution time, which enables complex applications running realistic data sets to be studied. The architecturalindependent information collected during the execution is fed to a mathematical cache model for predicting the cache miss ratio. The sparsely-collected data can be used to characterize the application’s data locality in respect to almost any possible cache hierarchy, such as complicated multiprocessor memory systems with multilevel cache hierarchies. Any combination of cache size, cache line size and degree of sharing can be modeled. Each new modeled design point takes only a fraction of a second to evaluate, even though the application from which the sampled data was collected may have executed for hours. This makes the tool not just usable for software developers, but also for hardware developers who need to evaluate a huge memory-system design space. We also discuss different ways of presenting data-locality information to a programmer in an intuitive and easily interpreted way. Some of the locality metrics we introduce utilize the flexibility of our algorithm and its ability to vary different cache parameters for one run. The dissertation also presents several prototype implementations of tools for profiling the memory system.
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| 30. |
- Collet, Julie M., et al.
(författare)
-
Rapid evolution of the intersexual genetic correlation for fitness in Drosophila melanogaster
- 2016
-
Ingår i: Evolution. - : Wiley. - 0014-3820 .- 1558-5646. ; 70:4, s. 781-795
-
Tidskriftsartikel (refereegranskat)abstract
- Sexual antagonism (SA) arises when male and female phenotypes are under opposing selection, yet genetically correlated. Until resolved, antagonism limits evolution toward optimal sex-specific phenotypes. Despite its importance for sex-specific adaptation and existing theory, the dynamics of SA resolution are not well understood empirically. Here, we present data from Drosophila melanogaster, compatible with a resolution of SA. We compared two independent replicates of the LHM population in which SA had previously been described. Both had been maintained under identical, controlled conditions, and separated for around 200 generations. Although heritabilities of male and female fitness were similar, the intersexual genetic correlation differed significantly, being negative in one replicate (indicating SA) but close to zero in the other. Using population sequencing, we show that phenotypic differences were associated with population divergence in allele frequencies at nonrandom loci across the genome. Large frequency changes were more prevalent in the population without SA and were enriched at loci mapping to genes previously shown to have sexually antagonistic relationships between expression and fitness. Our data suggest that rapid evolution toward SA resolution has occurred in one of the populations and open avenues toward studying the genetics of SA and its resolution.
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| 31. |
- Crossley, I. R., et al.
(författare)
-
Synthesis of the ruthenaboratranes Ru(CS)(PPh3){B(mt)(3)} (Ru -> B)(8) and Ru(CO)(CNR){B(mt)(3)} (Ru -> B)(8) (mt = methimazolyl, R = Bu-t, C6H3Me2-2,6, C6H2Me3-2,4,6)
- 2008
-
Ingår i: Organometallics. - : American Chemical Society (ACS). - 0276-7333 .- 1520-6041. ; 27:3, s. 381-386
-
Tidskriftsartikel (refereegranskat)abstract
- The reaction of [Ru(CH=CH2)Cl(CS)(PPh3)(2)] with Na[HB(mt)(3)] (mt = methimazolyl) provides the ruthenaboratrane [Ru(CS)(PPh3){B(mt)(3)}]. The reaction of [Ru(CO)(PPh3){B(mt)3}] with CO to provide [Ru(CO)(2){B(mt)(3)}] is reversible, while the phosphine-free ruthenaboratranes [Ru(CO)(CNR){B(mt(3))}] (R = Bu-t, C6H3Me2-2,6, C6H2Me3-2,4,6) form irreversibly upon addition of isonitriles (CNR) to [Ru(CO)(PPh3){B(mt)(3)}]. The crystal structures of the ruthenaboratranes [Ru(CS)(PPh3){B(mt)(3)}], [Ru(CO)((CNBu)-Bu-t)({B(mt)(3)}], and [Ru(CO)(CNC6H2Me3-2,4,6){B(mt)(3)}] are reported.
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| 32. |
- Crossley, I. R., et al.
(författare)
-
The first rhodaboratrane: RhCl(PPh3){B(mt)(3)} (Rh -> B) (mt = methimazolyl)
- 2005
-
Ingår i: Chemical Communications. - : Royal Society of Chemistry (RSC). - 1364-548X .- 1359-7345. ; :2, s. 221-223
-
Tidskriftsartikel (refereegranskat)abstract
- The reaction of [Rh(C6H5)Cl-2(PPh3)(2)] with Na[HB(mt)(3)] (mt = methimazolyl) provides [RhCl(PPh3){B(mt)(3)}](Rh-->B) the first authentic example of a compound with a rhodium boron dative bond.
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| 33. |
- Cuthill, Innes C., et al.
(författare)
-
The biology of color
- 2017
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 357:6350
-
Forskningsöversikt (refereegranskat)abstract
- Coloration mediates the relationship between an organism and its environment in important ways, including social signaling, antipredator defenses, parasitic exploitation, thermoregulation, and protection from ultraviolet light, microbes, and abrasion. Methodological breakthroughs are accelerating knowledge of the processes underlying both the production of animal coloration and its perception, experiments are advancing understanding of mechanism and function, and measurements of color collected noninvasively and at a global scale are opening windows to evolutionary dynamics more generally. Here we provide a roadmap of these advances and identify hitherto unrecognized challenges for this multi- and interdisciplinary field.
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| 34. |
- Diaz, Sandra, et al.
(författare)
-
The IPBES Conceptual Framework - connecting nature and people
- 2015
-
Ingår i: Current Opinion in Environmental Sustainability. - : Elsevier BV. - 1877-3435 .- 1877-3443. ; 14, s. 1-16
-
Tidskriftsartikel (refereegranskat)abstract
- The first public product of the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES) is its Conceptual Framework. This conceptual and analytical tool, presented here in detail, will underpin all IPBES functions and provide structure and comparability to the syntheses that IPBES will produce at different spatial scales, on different themes, and in different regions. Salient innovative aspects of the IPBES Conceptual Framework are its transparent and participatory construction process and its explicit consideration of diverse scientific disciplines, stakeholders, and knowledge systems, including indigenous and local knowledge. Because the focus on co-construction of integrative knowledge is shared by an increasing number of initiatives worldwide, this framework should be useful beyond IPBES, for the wider research and knowledge-policy communities working on the links between nature and people, such as natural, social and engineering scientists, policy-makers at different levels, and decision-makers in different sectors of society.
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| 35. |
- Foreman, Mark, 1973, et al.
(författare)
-
Metallathiirenes. 5. Bis- and tris(methimazolyl)borato thiocarbamoyl complexes of molybdenum(II)
- 2003
-
Ingår i: Organometallics. - : American Chemical Society (ACS). - 0276-7333 .- 1520-6041. ; 22:26, s. 5593-5596
-
Tidskriftsartikel (refereegranskat)abstract
- Thiocarbamoyl complexes [Mo(eta(2)-SCNMe2)-(CO)(2){HnB(mt)(4-n)}] (n = 1, 2) are obtained from the reactions of [Mo(eta(2)-SCNMe2)Cl(CO)(2)(tmeda)]andNa[HnB(mt)(4-n)] or via reactions of the salts Na[Mo(CO)(2+n){HnB(mt)(4-n)}] with Me2NCSCl. For n = 2, the complex displays agostic B-H-Mo coordination in both solution and the solid state.
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| 36. |
- Foreman, Mark, 1973, et al.
(författare)
-
Novel heterobimetallic coordination of the H2B(mt)(2) ligand: The complex Mo(SnMe2Cl)(CO)(3){mu-S : K-3 -H,S,S '-H2B(mt)2} (mt = methimazolyl)
- 2005
-
Ingår i: Organometallics. - : American Chemical Society (ACS). - 0276-7333 .- 1520-6041. ; 24:22, s. 5224-5226
-
Tidskriftsartikel (refereegranskat)abstract
- Molybdenum stannyl complexes ligated by poly(methimazolyl)borate ligands are accessible via complementary strategies involving oxidative addition of either Ph3Sn{HB(mt)(3)} (mt = methimazolyl) or [Me2Sn{H2B(Mt)(2)}]Cl to molybdenum(0) precursors or alternatively via reactions of halostannanes with the salts Na[Mo(CO)(3){HxB(mt)(4-x)}] (x = 1, 2). One example provides a novel complex in which the H2B(Mt)(2) ligand bridges both molybdenum and tin, thereby providing a model for an intermediate in the oxidative addition protocol.
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| 37. |
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| 38. |
- Foreman, Mark, 1973, et al.
(författare)
-
Synthesis and ligand substitution reactions of κ 4 -B,S,S',S''-ruthenaboratranes
- 2019
-
Ingår i: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; 48:1, s. 209-219
-
Tidskriftsartikel (refereegranskat)abstract
- A range of ruthenaboratranes of the form [Ru(CO)L{κ4-B,S,S',S''-B(mt)3}] (mt = N-methylmercaptoimidazolyl) have been prepared either by substitution of the PPh3 ligand in [Ru(CO)(PPh3){κ4-B,S,S',S''-B(mt)3}] by L (L = PMe2Ph, PMe3, P(OMe)3, P(OEt)3, P(OPh)3) or reactions of [RuCl(R)(CO)Ln] (R = Ph, CH[double bond, length as m-dash]CHPh; n = 2, L = PCy3; n = 3, L = P(OMe)3, PMe2Ph) with Na[HB(mt)3].
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| 39. |
- Gomez, Maria, et al.
(författare)
-
Opposing actions of inositol 1,4,5-trisphosphate and ryanodine receptors on nuclear factor of activated T-cells regulation in smooth muscle
- 2002
-
Ingår i: Journal of Biological Chemistry. - 1083-351X. ; 277:40, s. 37756-37764
-
Tidskriftsartikel (refereegranskat)abstract
- The nuclear factor of activated T-cells (NFAT), originally identified in T-cells, has since been shown to play a role in mediating Ca(2+)-dependent gene transcription in diverse cell types outside of the immune system. We have previously shown that nuclear accumulation of NFATc3 is induced in ileal smooth muscle by platelet-derived growth factor in a manner that depends on Ca(2+) influx through L-type, voltage-dependent Ca(2+) channels. Here we show that NFATc3 is also the predominant NFAT isoform expressed in cerebral artery smooth muscle and is induced to accumulate in the nucleus by UTP and other G(q/11)-coupled receptor agonists. This induction is mediated by calcineurin and is dependent on sarcoplasmic reticulum Ca(2+) release through inositol 1,4,5-trisphosphate receptors and extracellular Ca(2+) influx through L-type, voltage-dependent Ca(2+) channels. Consistent with results obtained in ileal smooth muscle, depolarization-induced Ca(2+) influx fails to induce NFAT nuclear accumulation in cerebral arteries. We also provide evidence that Ca(2+) release by ryanodine receptors in the form of Ca(2+) sparks may exert an inhibitory influence on UTP-induced NFATc3 nuclear accumulation and further suggest that UTP may act, in part, by inhibiting Ca(2+) sparks. These results are consistent with a multifactorial regulation of NFAT nuclear accumulation in smooth muscle that is likely to involve several intracellular signaling pathways, including local effects of sarcoplasmic reticulum Ca(2+) release and effects attributable to global elevations in intracellular Ca(2+).
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| 40. |
- Goodsir, Freya, et al.
(författare)
-
A standardised approach to the environmental risk assessment of potentially polluting wrecks
- 2019
-
Ingår i: Marine Pollution Bulletin. - : Elsevier BV. - 0025-326X .- 1879-3363. ; 142, s. 290-302
-
Tidskriftsartikel (refereegranskat)abstract
- The potential risk to the marine environment of oil release from potentially polluting wrecks (PPW) is increasingly being acknowledged, and in some instances remediation actions have been required. However, where a PPW has been identified, there remains a great deal of uncertainty around the environmental risk it may pose. Estimating the likelihood of a wreck to release oil and the threat to marine receptors remains a challenge. In addition, removing oil from wrecks is not always cost effective, so a proactive approach is recommended to identify PPW that pose the greatest risk to sensitive marine ecosystems and local economies and communities. This paper presents a desk-based assessment approach which addresses PPW, and the risk they pose to environmental and socio-economic marine receptors, using modelled scenarios and a framework and scoring system. This approach can be used to inform proactive management options for PPW and can be applied worldwide.
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| 41. |
- Griffith, Simon C., et al.
(författare)
-
Variation in reproductive success across captive populations: Methodological differences, potential biases and opportunities
- 2017
-
Ingår i: Ethology. - : Wiley. - 1439-0310 .- 0179-1613. ; 123:1, s. 1-29
-
Tidskriftsartikel (refereegranskat)abstract
- Our understanding of fundamental organismal biology has been disproportionately influenced by studies of a relatively small number of ‘model’ species extensively studied in captivity. Laboratory populations of model species are commonly subject to a number of forms of past and current selection that may affect experimental outcomes. Here, we examine these processes and their outcomes in one of the most widely used vertebrate species in the laboratory – the zebra finch (Taeniopygia guttata). This important model species is used for research across a broad range of fields, partly due to the ease with which it can be bred in captivity. However despite this perceived amenability, we demonstrate extensive variation in the success with which different laboratories and studies bred their subjects, and overall only 64% of all females that were given the opportunity, bred successfully in the laboratory. We identify and review several environmental, husbandry, life-history and behavioural factors that potentially contribute to this variation. The variation in reproductive success across individuals could lead to biases in experimental outcomes and drive some of the heterogeneity in research outcomes across studies. The zebra finch remains an excellent captive animal system and our aim is to sharpen the insight that future studies of this species can provide, both to our understanding of this species and also with respect to the reproduction of captive animals more widely. We hope to improve systematic reporting methods and that further investigation of the issues we raise will lead both to advances in our fundamental understanding of avian reproduction as well as to improvements in future welfare and experimental efficiency.
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| 42. |
- Haywood, Alan M., et al.
(författare)
-
The Pliocene Model Intercomparison Project Phase 2 : large-scale climate features and climate sensitivity
- 2020
-
Ingår i: Climate of the Past. - : Copernicus GmbH. - 1814-9324 .- 1814-9332. ; 16:6, s. 2095-2123
-
Tidskriftsartikel (refereegranskat)abstract
- The Pliocene epoch has great potential to improve our understanding of the long-term climatic and environmental consequences of an atmospheric CO2 concentration near similar to 400 parts per million by volume. Here we present the large-scale features of Pliocene climate as simulated by a new ensemble of climate models of varying complexity and spatial resolution based on new reconstructions of boundary conditions (the Pliocene Model Intercomparison Project Phase 2; PlioMIP2). As a global annual average, modelled surface air temperatures increase by between 1.7 and 5.2 degrees C relative to the pre-industrial era with a multi-model mean value of 3.2 degrees C. Annual mean total precipitation rates increase by 7 % (range: 2 %-13 %). On average, surface air temperature (SAT) increases by 4.3 degrees C over land and 2.8 degrees C over the oceans. There is a clear pattern of polar amplification with warming polewards of 60 degrees N and 60 degrees S exceeding the global mean warming by a factor of 2.3. In the Atlantic and Pacific oceans, meridional temperature gradients are reduced, while tropical zonal gradients remain largely unchanged. There is a statistically significant relationship between a model's climate response associated with a doubling in CO2 (equilibrium climate sensitivity; ECS) and its simulated Pliocene surface temperature response. The mean ensemble Earth system response to a doubling of CO2 (including ice sheet feedbacks) is 67 % greater than ECS; this is larger than the increase of 47 % obtained from the PlioMIP1 ensemble. Proxy-derived estimates of Pliocene sea surface temperatures are used to assess model estimates of ECS and give an ECS range of 2.6-4.8 degrees C. This result is in general accord with the ECS range presented by previous Intergovernmental Panel on Climate Change (IPCC) Assessment Reports.
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| 43. |
- Hill, Emma M., et al.
(författare)
-
Combination of geodetic observations and models for glacial isostatic adjustment fields in Fennoscandia
- 2010
-
Ingår i: Journal of Geophysical Research. - 0148-0227 .- 2156-2202. ; 115:B07
-
Tidskriftsartikel (refereegranskat)abstract
- We demonstrate a new technique for using geodetic data to update a priori predictionsfor Glacial Isostatic Adjustment (GIA) in the Fennoscandia region. Global PositioningSystem (GPS), tide gauge, and Gravity Recovery and Climate Experiment (GRACE)gravity rates are assimilated into our model. The technique allows us to investigate theindividual contributions from these data sets to the output GIA model in a self‐consistentmanner. Another benefit of the technique is that we are able to estimate uncertaintiesfor the output model. These are reduced with each data set assimilated. Any uncertaintiesin the GPS reference frame are absorbed by reference frame adjustments that are estimatedas part of the assimilation. Our updated model shows a spatial pattern and magnitudeof peak uplift that is consistent with previous models, but our location of peak upliftis slightly to the east of many of these. We also simultaneously estimate a spatiallyaveraged rate of local sea level rise. This regional rate (∼1.5 mm/yr) is consistent forall solutions, regardless of which data sets are assimilated or the magnitude of a priori GPSreference frame constraints. However, this is only the case if a uniform regional gravityrate, probably representing errors in, or unmodeled contributions to, the low‐degreeharmonic terms from GRACE, is also estimated for the assimilated GRACE data. Ourestimated sea level rate is consistent with estimates obtained using a more traditionalapproach of direct “correction” using collocated GPS and tide gauge sites.
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| 44. |
- Hill, Timothy A., et al.
(författare)
-
Iminochromene Inhibitors of Dynamins I and II GTPase Activity and Endocytosis
- 2010
-
Ingår i: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 53:10, s. 4094-4102
-
Tidskriftsartikel (refereegranskat)abstract
- Herein we report the synthesis of discrete iminochromene (“iminodyn”) libraries (14−38) as potential inhibitors of dynamin GTPase. Thirteen iminodyns were active (IC50 values of 260 nM to 100 μM), with N,N-(ethane-1,2-diyl)bis(7,8-dihydroxy-2-iminochromene-3-carboxamide) (17), N,N-(ethane-1,2-diyl)bis(7,8-dihydroxy-2-iminochromene-3-carboxamide) (22), and N,N-(ethane-1,2-diyl)bis(7,8-dihydroxy-2-iminochromene-3-carboxamide) (23) (IC50 values of 330 ± 70, 450 ± 50, and 260 ± 80 nM, respectively) being the most potent. Five of the most potent iminodyns all inhibited dynamins I and II approximately equally. Iminodyn-22 displayed uncompetitive inhibition with respect to GTP. Selected iminodyns were evaluated for their ability to block receptor mediated endocytosis (RME, mediated by dynamin II) and synaptic vesicle endocytosis (SVE, mediated by dynamin I), with 17 showing no activity while 22 returned RME and SVE IC50 values of 10.7 ± 4.5 and 99.5 ± 1.7 μM, respectively. The iminodyns reported herein represent a new chemical class of the first nanomolar potent dynamin inhibitors that are also effective endocytosis inhibitors.
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| 45. |
- Hill, Tobias, 1975-
(författare)
-
Development of New Methods for Inferring and Evaluating Phylogenetic Trees
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Inferring phylogeny is a difficult computational problem. Heuristics are necessary to minimize the time spent evaluating non optimal trees. In paper I, we developed an approach for heuristic searching, using a genetic algorithm. Genetic algorithms mimic the natural selections ability to solve complex problems. The algorithm can reduce the time required for weighted maximum parsimony phylogenetic inference using protein sequences, especially for data sets involving large number of taxa. Evaluating and comparing the ability of phylogenetic methods to infer the correct topology is complex. In paper II, we developed software that determines the minimum subtree prune and regraft (SPR) distance between binary trees to ease the process. The minimum SPR distance can be used to measure the incongruence between trees inferred using different methods. Given a known topology the methods could be evaluated on their ability to infer the correct phylogeny given specific data. The minimum SPR software the intermediate trees that separate two binary trees. In paper III we developed software that given a set of incongruent trees determines the median SPR consensus tree i.e. the tree that explains the trees with a minimum of SPR operations. We investigated the median SPR consensus tree and its possible interpretation as a species tree given a set of gene trees. We used a set of α-proteobacteria gene trees to test the ability of the algorithm to infer a species tree and compared it to previous studies. The results show that the algorithm can successfully reconstruct a species tree.Expressed sequence tag (EST) data is important in determining intron-exon boundaries, single nucleotide polymorphism and the coding sequence of genes. In paper IV we aligned ESTs to the genome to evaluate the quality of EST data. The results show that many ESTs are contaminated by vector sequences and low quality regions. The reliability of EST data is largely determined by the clustering of the ESTs and the association of the clusters to the correct portion of genome. We investigate the performance of EST clustering using the genome as template compared to previously existing methods using pair-wise alignments. The results show that using the genome as guidance improves the resulting EST clusters in respect to the extent ESTs originating from the same transcriptional unit are separated into disjunct clusters.
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| 46. |
- Hill, Timothy, et al.
(författare)
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Small molecule inhibitors of dynamin I GTPase activity : development of dimeric tyrphostins.
- 2005
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Ingår i: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 48:24
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Tidskriftsartikel (refereegranskat)abstract
- Dynamin I is a GTPase enzyme required for endocytosis and is an excellent target for the design of potential endocytosis inhibitors. Screening of a library of tyrphostins, in our laboratory, against the GTPase activity of dynamin I gave rise to a microM potent lead, 2-cyano-3-(3,4-dihydroxyphenyl)thioacrylamide (1, IC50 70 microM). Our initial investigations suggested that only the dimeric form of 1 displayed dynamin I GTPase inhibitory activity. Subsequent synthetic iterations were based on dimeric analogues and afforded a number of small molecules, low microM potent, inhibitors of dynamin I GTPase, in particular, symmetrical analogues with a minimum of two free phenolic -OHs: catechol-acrylamide (9) (IC50= 5.1 +/- 0.6 microM), its 3,4,5-trihydroxy congener (10) (IC50= 1.7 +/- 0.2 microM), and the corresponding 3-methyl ether (11) (IC50= 9 +/- 3 microM). Increasing the length of the central alkyl spacer from ethyl to propyl (22-24) afforded essentially identical activity with IC50's of 1.7 +/- 0.2, 1.7 +/- 0.2, and 5 +/- 1 microM, respectively. No decrease in activity was noted until the introduction of a hexyl spacer. Our studies highlight the requirement for two free amido NHs with neither the mono-N-methyl (86) nor the bis-N-methyl (87) analogues inhibiting dynamin I GTPase. A similar effect was noted for the removal of the nitrile moieties. However, modest potency was observed with the corresponding ester analogues of 9-11: ethyl ester (90), propyl ester (91), and butyl ester (92), with IC50's of 42 +/- 3, 38 +/- 2, and 61 +/- 2 microM, respectively. Our studies reveal the most potent and promising dynamin I GTPase inhibitor in this series as (22), which is also known as BisT.
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| 47. |
- Howes, Mark T, et al.
(författare)
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Clathrin-independent carriers form a high capacity endocytic sorting system at the leading edge of migrating cells
- 2010
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Ingår i: Journal of Cell Biology. - : Rockefeller University Press. - 0021-9525 .- 1540-8140. ; 190:4, s. 675-691
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Tidskriftsartikel (refereegranskat)abstract
- Although the importance of clathrin- and caveolin-independent endocytic pathways has recently emerged, key aspects of these routes remain unknown. Using quantitative ultrastructural approaches, we show that clathrin-independent carriers (CLICs) account for approximately three times the volume internalized by the clathrin-mediated endocytic pathway, forming the major pathway involved in uptake of fluid and bulk membrane in fibroblasts. Electron tomographic analysis of the 3D morphology of the earliest carriers shows that they are multidomain organelles that form a complex sorting station as they mature. Proteomic analysis provides direct links between CLICs, cellular adhesion turnover, and migration. Consistent with this, CLIC-mediated endocytosis of key cargo proteins, CD44 and Thy-1, is polarized at the leading edge of migrating fibroblasts, while transient ablation of CLICs impairs their ability to migrate. These studies provide the first quantitative ultrastructural analysis and molecular characterization of the major endocytic pathway in fibroblasts, a pathway that provides rapid membrane turnover at the leading edge of migrating cells.
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| 48. |
- Jentes, Emily S, et al.
(författare)
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The revised global yellow fever risk map and recommendations for vaccination, 2010 : consensus of the Informal WHO Working Group on geographic risk for Yellow Fever.
- 2011
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Ingår i: The Lancet - Infectious diseases. - : Elsevier. - 1473-3099 .- 1474-4457. ; 11:8, s. 622-632
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Tidskriftsartikel (refereegranskat)abstract
- The changing epidemiology of yellow fever and continued reports of rare but serious adverse events associated with yellow fever vaccine have drawn attention to the need to revisit criteria for the designation of areas with risk for yellow fever virus activity, and to revise the vaccine recommendations for international travel. WHO convened a working group of international experts to review factors important for the transmission of yellow fever virus and country-specific yellow fever information, to establish criteria for additions to or removal from the list of countries with risk for yellow fever virus transmission, to update yellow fever risk maps, and to revise the recommendations for vaccination for international travel. This report details the recommendations made by the working group about criteria for the designation of risk and specific changes to the classification of areas with risk for transmission of yellow fever virus.
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| 49. |
- Kimber, Simon A. J., et al.
(författare)
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Charge Order at the Frontier between the Molecular and Solid States in Ba3NaRu2O9
- 2012
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Ingår i: Physical Review Letters. - 1079-7114. ; 108:21
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Tidskriftsartikel (refereegranskat)abstract
- We show that the valence electrons of Ba3NaRu2O9, which has a quasimolecular structure, completely crystallize below 210 K. Using an extended Hubbard model, we show that the charge ordering instability results from long-range Coulomb interactions. However, orbital ordering, metal-metal bonding, and formation of a partial spin gap enforce the magnitude of the charge separation. The striped charge order and frustrated hcp lattice of Ru2O9 dimers lead to competition with a quasidegenerate charge-melted phase under photoexcitation at low temperature. Our results establish a broad class of simple metal oxides as models for emergent phenomena at the border between the molecular and solid states.
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| 50. |
- Lai, Qiwen, et al.
(författare)
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Hydrogen Storage Materials for Mobile and Stationary Applications : Current State of the Art
- 2015
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Ingår i: ChemSusChem. - : Wiley. - 1864-5631 .- 1864-564X. ; 8:17, s. 2789-2825
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Tidskriftsartikel (refereegranskat)abstract
- One of the limitations to the widespread use of hydrogen as an energy carrier is its storage in a safe and compact form. Herein, recent developments in effective high-capacity hydrogen storage materials are reviewed, with a special emphasis on light compounds, including those based on organic porous structures, boron, nitrogen, and aluminum. These elements and their related compounds hold the promise of high, reversible, and practical hydrogen storage capacity for mobile applications, including vehicles and portable power equipment, but also for the large scale and distributed storage of energy for stationary applications. Current understanding of the fundamental principles that govern the interaction of hydrogen with these light compounds is summarized, as well as basic strategies to meet practical targets of hydrogen uptake and release. The limitation of these strategies and current understanding is also discussed and new directions proposed.
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